Author's Accepted Manuscript
Haplotype-tag single nucleotide polymorphism analysis of the vesicular glutamate transporter (VGLUT) genes in severely alcoholic women Erika Comasco, Jarmila Hallman, Åsa WallénMackenzie
www.elsevier.com/locate/psychres
PII: DOI: Reference:
S0165-1781(14)00472-7 http://dx.doi.org/10.1016/j.psychres.2014.05.052 PSY8322
To appear in:
Psychiatry Research
Cite this article as: Erika Comasco, Jarmila Hallman, Åsa Wallén-Mackenzie, Haplotype-tag single nucleotide polymorphism analysis of the vesicular glutamate transporter (VGLUT) genes in severely alcoholic women, Psychiatry Research, http://dx.doi.org/10.1016/j.psychres.2014.05.052 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
VGLUT genes and alcoholism Haplotype‐tag single nucleotide polymorphism analysis of the Vesicular Glutamate Transporter (VGLUT) genes in severely alcoholic women To the Editor: Dysfunctions of the glutamatergic system has been associated with alcohol‐related phenotypes. Acamprosate, which targets this system, is used clinically as treatment for alcoholism. Glutamate‐transmitting neurons can be identified and defined by their expression of Vesicular Glutamate Transporter (VGLUT) genes that belong to the Solute Carrier Family 17 and code for sodium‐ dependent phosphate transporter proteins. Three subtypes of VGLUTs (VGLUT1 encoded by SLC17A7; VGLUT2 by SLC17A6; and VGLUT3 by SLC17A8) are known to date to mediate presynaptic vesicular transport of glutamate. Alcohol Use Disorder is a multi‐factorial disorder with a moderate heritability as demonstrated by studies of twins. The present study aimed at investigating common haplotype tag‐ single nucleotide polymorphism (SNP) in the VLGUT1, VGLUT2 and VLGUT3 genes in a sample of severely alcoholic women compared to healthy controls. A sample of 191 female patients admitted upon court order to a long‐term treatment facility for severe alcoholism was recruited. All patients fulfilled the ICD‐10 Diagnostic Criteria for alcohol dependence. A control sample of 184 women without self‐reported history of alcoholism or present heavy drinking was included. All participants self‐reported a Swedish ethnical background. Haplotype tag‐SNPs in the VGLUT1, VGLUT2 and VGLUT3 genes were analysed (minimum minor allele frequency of 0.1; r2 ≥ 0.8, pairwise tagging only). Totally, 13 tagSNPs were selected which tagged 30 SNPs in the SLC17A6 gene; 7 tagSNPs which tagged 12 SNPs in the SLC17A7 gene; 11 tagSNPs which tagged 45 SNPs in the SLC17A8 gene (Table 1). At the single locus‐ analysis level, the SNP rs2290045 (SLC17A6/VGLUT2) showed a significant nominal association with severe alcoholism in a dominant model (p = 0.034; OR = 1.660, lower CI = 1.036 and higher CI = 2.658), with the minor allele A being overrepresented among patients (minor allele count: cases = 57 and controls = 43). The same marker was also the only one showing borderline significance in an additive model evaluated with the Cochran Armitage test (p = 0.077; GA vs. GG, OR = 1.762, lower CI = 1.090 and higher CI = 2.849); and in an allelic model (p = 0.087; A allele, OR = 1.448, lower CI = 0.946 and higher CI = 2.216). However none of the associations was significant after Bonferroni correction for multiple testing. At the multi‐locus gene level, backward and forward stepwise regression models indicated the SNP rs2290045 (OR = 2.390) and also rs1900586 (SLC17A6/VGLUT2; OR = 0.402) as significant regressors (p = 0.014), however the permuted p‐value (100x) was not remaining significant. The SNPs showed low linkage disequilibrium (R2) between each other, as expected, and no haplotypes were detected as estimated with the EM algorithm (Figure 1). 1
VGLUT genes and alcoholism The VGLUT proteins mediate the packaging of glutamate into presynaptic vesicles, a prerequisite for exocytotic release, and therefore, the expression of either of the genes encoding a VGLUT in a neuron defines its ability for glutamatergic neurotransmission (El Mestikawy, Wallen‐Mackenzie, Fortin, Descarries, & Trudeau 2011). The importance of glutamatergic neurons in addiction has been substantially studied and described. It has been established that cortical glutamatergic neurons, among others, enhance mesocorticolimbic dopamine transmission by direct interaction with the dopaminergic neurons, a feature shown to contribute to mediating alcohol‐induced reinforcement. In addition, certain aminergic neurons (cholinergic, serotonergic and dopaminergic) exhibit a glutamate co‐phenotype via their expression of VGLUT2 or VGLUT3, a phenomenon of putative relevance for mediating the effects of alcohol (El Mestikawy et al. 2011). The presence of VGLUT proteins in presynaptic vesicles of aminergic neurons has been described to enable glutamate co‐release as well as promote elevated efficiency for vesicular packaging of the primary neurotransmitter itself (El Mestikawy et al. 2011). Moreover, mice lacking VGLUT2 in midbrain dopamine neurons have been shown to display altered response to acute injections of amphetamine (Birgner et al. 2010) and cocaine (Hnasko et al. 2010), as well as enhanced cocaine self‐administration and cue‐induced drug seeking, a behavioural correlate of craving in human addicts (Alsio et al. 2011). The present study tested the hypothesis that common variations in the VGLUT genes would be associated with severe alcoholism, and indicated one haplotype tag‐SNP, rs2290045, in an intronic region of the VGLUT2 gene, which is mapped to chromosome 11p14. Previous studies show evidence of an association between loci at the chromosome 11 and alcohol dependence. Potential epistatic effects are also likely to be of importance, as for instance, one polymorphism in the Period2 (PER2) gene, which is influencing the glutamate aspartate transporter, has been associated with alcohol use and misuse (Comasco et al. 2010). The identification of the haplotype tag‐SNP, rs2290045, in the VGLUT2 gene, as nominally associated with severe alcoholism among females was the predominant finding of the study, however the association was not found significant after correction for multiple testing. The small sample size is the major limitation of the present study, as well as the lack of a male sample to analyze for sex differences; thus we would suggest further studies in larger samples of both sexes to overcome the uncertainty on statistical and biological significance. Moreover, gene‐wide sequencing studies to investigate rare variants are also warranted, as well as relevant genetic animal models that enable further analysis of the putative role of VGLUTs in alcohol addiction.
2
VGLUT genes and alcoholism Acknowledgements:The authors thank the participants, as well as Assoc. Prof. Skalkidou Alkistis and Prof. Sundström‐Poromaa Inger, Department of Women’s & Children’s Health, Uppsala University, for providing the biological material for the control sample. This work was supported by grants from the Swedish Council for Working Life and Social Research to E.C. (2011‐0627), and from the Swedish Medical Research Council (2007‐5742, 2011‐4747), Uppsala University, the Swedish Brain Foundation and the foundations of Åke Wiberg and Åhlén to Å.W.M. References Alsiö, J., Nordenankar, K., Arvidsson, E., Birgner, C., Mahmoudi, S., Halbout, B., Smith, C., Fortin, G. M., Olson, L., Descarries, L., Trudeau, L. E., Kullander, K., Levesque, D. & Wallén‐Mackenzie, A. (2011) Enhanced sucrose and cocaine self‐administration and cue‐induced drug seeking after loss of VGLUT2 in midbrain dopamine neurons in mice. J Neurosci 31(35): 12593‐12603. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2 1880920 Birgner, C., Nordenankar, K., Lundblad, M., Mendez, J. A., Smith, C., le Greves, M., Galter, D., Olson, L., Fredriksson, A., Trudeau, L. E., Kullander, K. & Wallén‐Mackenzie, A. (2010) VGLUT2 in dopamine neurons is required for psychostimulant‐induced behavioral activation. Proc Natl Acad Sci U S A 107(1): 389‐394. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2 0018672 Comasco, E., Nordquist, N., Gokturk, C., Aslund, C., Hallman, J., Oreland, L. & Nilsson, K. W. (2010) The clock gene PER2 and sleep problems: association with alcohol consumption among Swedish adolescents. Ups J Med Sci 115(1): 41‐48. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2 0187847 El Mestikawy, S., Wallén‐Mackenzie, A., Fortin, G. M., Descarries, L. & Trudeau, L. E. (2011) From glutamate co‐release to vesicular synergy: vesicular glutamate transporters. Nat Rev Neurosci 12(4): 204‐216. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2 1415847 Hnasko, T. S., Chuhma, N., Zhang, H., Goh, G. Y., Sulzer, D., Palmiter, R. D., Rayport, S. & Edwards, R. H. (2010) Vesicular glutamate transport promotes dopamine storage and glutamate corelease in vivo. Neuron 65(5): 643‐656. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2 0223200 Erika Comasco, Jarmila Hallman, Åsa Wallén‐Mackenzie* Department of Neuroscience, Uppsala University, Sweden * Corresponding author: Uppsala University, Department of Neuroscience, BMC, Box 593, SE‐75124, Uppsala, Sweden; telephone: 0046 (0)18 471 4518; e‐mail: [email protected]
3
VGLUT genes and alcoholism Table 1 Chromosomal position, allele and genotype frequencies of the analysed tag-SNPs in the VGLUT1, VGLUT2 and VGLUT3 genes MARK ER
LOCATION
CAL L RAT E
(dbSNP) Chromoso Position Associat me (NCBI) ed gene
rs104355 8 rs382671 8 rs291465 8 rs132030 1 rs116728 10 rs157894 4 rs129755 98
19
rs259369 6 rs144751 4 rs227875 1 rs266569 1 rs110265 29 rs110265 31 rs229004 6 rs229004 5 rs115533 1 rs190058 6 rs108337 48 rs259368 5 rs197907 2
11
rs123727 48 rs108605 82 rs731117 8 rs797335 0 rs476473 8 rs111103 56
19 19 19 19 19 19
11 11 11 11 11 11 11 11 11 11 11 11
12 12 12 12 12 12
ALLELES
ALLELE FREQUENC IES Minor allele (D) Cas Contr es ols
FISHE R'S HWE p
GENOTYPE FREQUENCIES
dd
Dd
DD
4993276 2 4994013 1 4994231 4 4994243 2 4994377 8 4994585 0 4994821 3
SLC17A 7 SLC17A 7 SLC17A 7 SLC17A 7 SLC17A 7 SLC17A 7 SLC17A 7
0,98
Maj or Allel e A
0,98
G
C
0,28
0,27
0,14
92
98
73
83
14
9
0,99
C
T
0,19
0,19
0,24
121
122
53
64
7
4
0,97
G
A
0,28
0,26
0,85
89
103
76
71
12
13
0,98
G
A
0,34
0,37
0,28
77
72
82
96
19
22
0,98
T
C
0,28
0,28
0,86
91
98
73
78
14
14
0,97
G
A
0,40
0,38
0,44
60
75
95
82
23
29
2235927 9 2236229 6 2236475 8 2237125 6 2237805 7 2237918 4 2238416 6 2238497 0 2238619 0 2238744 0 2238774 5 2239141 9 2240012 4
SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6
0,98
G
A
0,21
0,22
0,83
116
112
57
67
9
8
0,98
G
A
0,12
0,14
0,55
138
140
38
44
3
5
0,96
G
A
0,47
0,44
0,30
48
54
88
101
37
33
0,97
G
A
0,30
0,32
0,04
89
80
71
94
18
13
0,98
G
A
0,10
0,10
0,38
144
155
37
30
0
3
0,98
C
T
0,22
0,24
0,05
105
115
66
59
7
16
0,97
C
T
0,11
0,13
0,54
139
140
37
46
0
2
0,98
G
A
0,16
0,11
0,72
124
147
55
37
1
3
0,99
G
A
0,29
0,26
0,19
91
106
75
66
15
17
0,98
A
G
0,14
0,16
0,26
128
133
49
55
1
2
0,98
T
C
0,38
0,37
0,04
65
83
92
74
23
32
0,98
A
G
0,41
0,41
0,77
56
64
98
94
25
31
0,98
C
A
0,16
0,17
0,61
124
127
55
56
2
4
1007495 25 1007509 52 1007551 02 1007631 66 1007722 30 1007736 47
SLC17A 8 SLC17A 8 SLC17A 8 SLC17A 8 SLC17A 8 SLC17A 8
0,95
A
T
0,14
0,17
0,30
126
124
46
57
1
3
0,98
T
C
0,17
0,19
0,10
124
120
47
67
6
3
0,97
C
G
0,27
0,28
1,00
95
94
74
76
11
14
0,95
G
T
0,45
0,46
0,77
47
52
98
94
29
37
0,91
A
G
0,50
0,47
0,65
36
50
93
84
37
41
0,96
C
T
0,31
0,31
0,31
76
86
88
87
9
15
Min or Allel e C
0,34
Control s
Cas es
Contr ols
Cas es
Contr ols
Cas es
Contr ols
0,30
0,23
78
95
82
73
20
21
4
VGLUT genes and alcoholism rs748548 0 rs202580 0 rs128266 43 rs943402 rs115685 37
12 12 12 12 12
1007809 19 1007810 29 1007818 88 1007929 79 1008139 76
SLC17A 8 SLC17A 8 SLC17A 8 SLC17A 8 SLC17A 8
0,97
G
A
0,30
0,26
0,19
86
106
77
65
15
16
0,98
C
A
0,40
0,40
0,30
64
65
86
99
28
27
0,95
C
T
0,42
0,41
0,54
55
61
95
93
26
28
0,97
A
G
0,15
0,16
1,00
127
131
49
50
2
4
0,98
A
C
0,46
0,47
0,66
52
56
88
91
39
43
Figure 1 Linkage disequilibrium (R2) plot of the tag-SNPs analyzed in the VGLUT1, VGLUT2 and VGLUT3 genes 5
VGLUT genes and alcoholism VGLUT1
VGLUT2
VGLUT3
6
Haplotype-tag single nucleotide polymorphism analysis of the vesicular glutamate transporter (VGLUT) genes in severely alcoholic women Erika Comasco, Jarmila Hallman, Åsa WallénMackenzie
www.elsevier.com/locate/psychres
PII: DOI: Reference:
S0165-1781(14)00472-7 http://dx.doi.org/10.1016/j.psychres.2014.05.052 PSY8322
To appear in:
Psychiatry Research
Cite this article as: Erika Comasco, Jarmila Hallman, Åsa Wallén-Mackenzie, Haplotype-tag single nucleotide polymorphism analysis of the vesicular glutamate transporter (VGLUT) genes in severely alcoholic women, Psychiatry Research, http://dx.doi.org/10.1016/j.psychres.2014.05.052 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
VGLUT genes and alcoholism Haplotype‐tag single nucleotide polymorphism analysis of the Vesicular Glutamate Transporter (VGLUT) genes in severely alcoholic women To the Editor: Dysfunctions of the glutamatergic system has been associated with alcohol‐related phenotypes. Acamprosate, which targets this system, is used clinically as treatment for alcoholism. Glutamate‐transmitting neurons can be identified and defined by their expression of Vesicular Glutamate Transporter (VGLUT) genes that belong to the Solute Carrier Family 17 and code for sodium‐ dependent phosphate transporter proteins. Three subtypes of VGLUTs (VGLUT1 encoded by SLC17A7; VGLUT2 by SLC17A6; and VGLUT3 by SLC17A8) are known to date to mediate presynaptic vesicular transport of glutamate. Alcohol Use Disorder is a multi‐factorial disorder with a moderate heritability as demonstrated by studies of twins. The present study aimed at investigating common haplotype tag‐ single nucleotide polymorphism (SNP) in the VLGUT1, VGLUT2 and VLGUT3 genes in a sample of severely alcoholic women compared to healthy controls. A sample of 191 female patients admitted upon court order to a long‐term treatment facility for severe alcoholism was recruited. All patients fulfilled the ICD‐10 Diagnostic Criteria for alcohol dependence. A control sample of 184 women without self‐reported history of alcoholism or present heavy drinking was included. All participants self‐reported a Swedish ethnical background. Haplotype tag‐SNPs in the VGLUT1, VGLUT2 and VGLUT3 genes were analysed (minimum minor allele frequency of 0.1; r2 ≥ 0.8, pairwise tagging only). Totally, 13 tagSNPs were selected which tagged 30 SNPs in the SLC17A6 gene; 7 tagSNPs which tagged 12 SNPs in the SLC17A7 gene; 11 tagSNPs which tagged 45 SNPs in the SLC17A8 gene (Table 1). At the single locus‐ analysis level, the SNP rs2290045 (SLC17A6/VGLUT2) showed a significant nominal association with severe alcoholism in a dominant model (p = 0.034; OR = 1.660, lower CI = 1.036 and higher CI = 2.658), with the minor allele A being overrepresented among patients (minor allele count: cases = 57 and controls = 43). The same marker was also the only one showing borderline significance in an additive model evaluated with the Cochran Armitage test (p = 0.077; GA vs. GG, OR = 1.762, lower CI = 1.090 and higher CI = 2.849); and in an allelic model (p = 0.087; A allele, OR = 1.448, lower CI = 0.946 and higher CI = 2.216). However none of the associations was significant after Bonferroni correction for multiple testing. At the multi‐locus gene level, backward and forward stepwise regression models indicated the SNP rs2290045 (OR = 2.390) and also rs1900586 (SLC17A6/VGLUT2; OR = 0.402) as significant regressors (p = 0.014), however the permuted p‐value (100x) was not remaining significant. The SNPs showed low linkage disequilibrium (R2) between each other, as expected, and no haplotypes were detected as estimated with the EM algorithm (Figure 1). 1
VGLUT genes and alcoholism The VGLUT proteins mediate the packaging of glutamate into presynaptic vesicles, a prerequisite for exocytotic release, and therefore, the expression of either of the genes encoding a VGLUT in a neuron defines its ability for glutamatergic neurotransmission (El Mestikawy, Wallen‐Mackenzie, Fortin, Descarries, & Trudeau 2011). The importance of glutamatergic neurons in addiction has been substantially studied and described. It has been established that cortical glutamatergic neurons, among others, enhance mesocorticolimbic dopamine transmission by direct interaction with the dopaminergic neurons, a feature shown to contribute to mediating alcohol‐induced reinforcement. In addition, certain aminergic neurons (cholinergic, serotonergic and dopaminergic) exhibit a glutamate co‐phenotype via their expression of VGLUT2 or VGLUT3, a phenomenon of putative relevance for mediating the effects of alcohol (El Mestikawy et al. 2011). The presence of VGLUT proteins in presynaptic vesicles of aminergic neurons has been described to enable glutamate co‐release as well as promote elevated efficiency for vesicular packaging of the primary neurotransmitter itself (El Mestikawy et al. 2011). Moreover, mice lacking VGLUT2 in midbrain dopamine neurons have been shown to display altered response to acute injections of amphetamine (Birgner et al. 2010) and cocaine (Hnasko et al. 2010), as well as enhanced cocaine self‐administration and cue‐induced drug seeking, a behavioural correlate of craving in human addicts (Alsio et al. 2011). The present study tested the hypothesis that common variations in the VGLUT genes would be associated with severe alcoholism, and indicated one haplotype tag‐SNP, rs2290045, in an intronic region of the VGLUT2 gene, which is mapped to chromosome 11p14. Previous studies show evidence of an association between loci at the chromosome 11 and alcohol dependence. Potential epistatic effects are also likely to be of importance, as for instance, one polymorphism in the Period2 (PER2) gene, which is influencing the glutamate aspartate transporter, has been associated with alcohol use and misuse (Comasco et al. 2010). The identification of the haplotype tag‐SNP, rs2290045, in the VGLUT2 gene, as nominally associated with severe alcoholism among females was the predominant finding of the study, however the association was not found significant after correction for multiple testing. The small sample size is the major limitation of the present study, as well as the lack of a male sample to analyze for sex differences; thus we would suggest further studies in larger samples of both sexes to overcome the uncertainty on statistical and biological significance. Moreover, gene‐wide sequencing studies to investigate rare variants are also warranted, as well as relevant genetic animal models that enable further analysis of the putative role of VGLUTs in alcohol addiction.
2
VGLUT genes and alcoholism Acknowledgements:The authors thank the participants, as well as Assoc. Prof. Skalkidou Alkistis and Prof. Sundström‐Poromaa Inger, Department of Women’s & Children’s Health, Uppsala University, for providing the biological material for the control sample. This work was supported by grants from the Swedish Council for Working Life and Social Research to E.C. (2011‐0627), and from the Swedish Medical Research Council (2007‐5742, 2011‐4747), Uppsala University, the Swedish Brain Foundation and the foundations of Åke Wiberg and Åhlén to Å.W.M. References Alsiö, J., Nordenankar, K., Arvidsson, E., Birgner, C., Mahmoudi, S., Halbout, B., Smith, C., Fortin, G. M., Olson, L., Descarries, L., Trudeau, L. E., Kullander, K., Levesque, D. & Wallén‐Mackenzie, A. (2011) Enhanced sucrose and cocaine self‐administration and cue‐induced drug seeking after loss of VGLUT2 in midbrain dopamine neurons in mice. J Neurosci 31(35): 12593‐12603. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2 1880920 Birgner, C., Nordenankar, K., Lundblad, M., Mendez, J. A., Smith, C., le Greves, M., Galter, D., Olson, L., Fredriksson, A., Trudeau, L. E., Kullander, K. & Wallén‐Mackenzie, A. (2010) VGLUT2 in dopamine neurons is required for psychostimulant‐induced behavioral activation. Proc Natl Acad Sci U S A 107(1): 389‐394. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2 0018672 Comasco, E., Nordquist, N., Gokturk, C., Aslund, C., Hallman, J., Oreland, L. & Nilsson, K. W. (2010) The clock gene PER2 and sleep problems: association with alcohol consumption among Swedish adolescents. Ups J Med Sci 115(1): 41‐48. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2 0187847 El Mestikawy, S., Wallén‐Mackenzie, A., Fortin, G. M., Descarries, L. & Trudeau, L. E. (2011) From glutamate co‐release to vesicular synergy: vesicular glutamate transporters. Nat Rev Neurosci 12(4): 204‐216. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2 1415847 Hnasko, T. S., Chuhma, N., Zhang, H., Goh, G. Y., Sulzer, D., Palmiter, R. D., Rayport, S. & Edwards, R. H. (2010) Vesicular glutamate transport promotes dopamine storage and glutamate corelease in vivo. Neuron 65(5): 643‐656. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=2 0223200 Erika Comasco, Jarmila Hallman, Åsa Wallén‐Mackenzie* Department of Neuroscience, Uppsala University, Sweden * Corresponding author: Uppsala University, Department of Neuroscience, BMC, Box 593, SE‐75124, Uppsala, Sweden; telephone: 0046 (0)18 471 4518; e‐mail: [email protected]
3
VGLUT genes and alcoholism Table 1 Chromosomal position, allele and genotype frequencies of the analysed tag-SNPs in the VGLUT1, VGLUT2 and VGLUT3 genes MARK ER
LOCATION
CAL L RAT E
(dbSNP) Chromoso Position Associat me (NCBI) ed gene
rs104355 8 rs382671 8 rs291465 8 rs132030 1 rs116728 10 rs157894 4 rs129755 98
19
rs259369 6 rs144751 4 rs227875 1 rs266569 1 rs110265 29 rs110265 31 rs229004 6 rs229004 5 rs115533 1 rs190058 6 rs108337 48 rs259368 5 rs197907 2
11
rs123727 48 rs108605 82 rs731117 8 rs797335 0 rs476473 8 rs111103 56
19 19 19 19 19 19
11 11 11 11 11 11 11 11 11 11 11 11
12 12 12 12 12 12
ALLELES
ALLELE FREQUENC IES Minor allele (D) Cas Contr es ols
FISHE R'S HWE p
GENOTYPE FREQUENCIES
dd
Dd
DD
4993276 2 4994013 1 4994231 4 4994243 2 4994377 8 4994585 0 4994821 3
SLC17A 7 SLC17A 7 SLC17A 7 SLC17A 7 SLC17A 7 SLC17A 7 SLC17A 7
0,98
Maj or Allel e A
0,98
G
C
0,28
0,27
0,14
92
98
73
83
14
9
0,99
C
T
0,19
0,19
0,24
121
122
53
64
7
4
0,97
G
A
0,28
0,26
0,85
89
103
76
71
12
13
0,98
G
A
0,34
0,37
0,28
77
72
82
96
19
22
0,98
T
C
0,28
0,28
0,86
91
98
73
78
14
14
0,97
G
A
0,40
0,38
0,44
60
75
95
82
23
29
2235927 9 2236229 6 2236475 8 2237125 6 2237805 7 2237918 4 2238416 6 2238497 0 2238619 0 2238744 0 2238774 5 2239141 9 2240012 4
SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6 SLC17A 6
0,98
G
A
0,21
0,22
0,83
116
112
57
67
9
8
0,98
G
A
0,12
0,14
0,55
138
140
38
44
3
5
0,96
G
A
0,47
0,44
0,30
48
54
88
101
37
33
0,97
G
A
0,30
0,32
0,04
89
80
71
94
18
13
0,98
G
A
0,10
0,10
0,38
144
155
37
30
0
3
0,98
C
T
0,22
0,24
0,05
105
115
66
59
7
16
0,97
C
T
0,11
0,13
0,54
139
140
37
46
0
2
0,98
G
A
0,16
0,11
0,72
124
147
55
37
1
3
0,99
G
A
0,29
0,26
0,19
91
106
75
66
15
17
0,98
A
G
0,14
0,16
0,26
128
133
49
55
1
2
0,98
T
C
0,38
0,37
0,04
65
83
92
74
23
32
0,98
A
G
0,41
0,41
0,77
56
64
98
94
25
31
0,98
C
A
0,16
0,17
0,61
124
127
55
56
2
4
1007495 25 1007509 52 1007551 02 1007631 66 1007722 30 1007736 47
SLC17A 8 SLC17A 8 SLC17A 8 SLC17A 8 SLC17A 8 SLC17A 8
0,95
A
T
0,14
0,17
0,30
126
124
46
57
1
3
0,98
T
C
0,17
0,19
0,10
124
120
47
67
6
3
0,97
C
G
0,27
0,28
1,00
95
94
74
76
11
14
0,95
G
T
0,45
0,46
0,77
47
52
98
94
29
37
0,91
A
G
0,50
0,47
0,65
36
50
93
84
37
41
0,96
C
T
0,31
0,31
0,31
76
86
88
87
9
15
Min or Allel e C
0,34
Control s
Cas es
Contr ols
Cas es
Contr ols
Cas es
Contr ols
0,30
0,23
78
95
82
73
20
21
4
VGLUT genes and alcoholism rs748548 0 rs202580 0 rs128266 43 rs943402 rs115685 37
12 12 12 12 12
1007809 19 1007810 29 1007818 88 1007929 79 1008139 76
SLC17A 8 SLC17A 8 SLC17A 8 SLC17A 8 SLC17A 8
0,97
G
A
0,30
0,26
0,19
86
106
77
65
15
16
0,98
C
A
0,40
0,40
0,30
64
65
86
99
28
27
0,95
C
T
0,42
0,41
0,54
55
61
95
93
26
28
0,97
A
G
0,15
0,16
1,00
127
131
49
50
2
4
0,98
A
C
0,46
0,47
0,66
52
56
88
91
39
43
Figure 1 Linkage disequilibrium (R2) plot of the tag-SNPs analyzed in the VGLUT1, VGLUT2 and VGLUT3 genes 5
VGLUT genes and alcoholism VGLUT1
VGLUT2
VGLUT3
6
